annotate hicQuickQC.xml @ 9:ea8fb5e899e8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:43:24 +0000
parents 21d859ad4502
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1 <tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>get a first quality estimate of Hi-C data</description>
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3 <macros>
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4 <token name="@BINARY@">hicQuickQC</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
0
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10 mkdir ./QCfolder &&
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11 mkdir $qc.files_path &&
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12 @BINARY@
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13
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14 --samFiles
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15 #for $repeat in $samFiles:
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16 '${repeat.samFile}'
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17 #end for
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18
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19 --restrictionCutFile '$restrictionCutFile'
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20
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21 #if $restrictionSequence:
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22 --restrictionSequence '$restrictionSequence'
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23 #end if
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24
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25 #if $danglingSequence:
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26 --danglingSequence '$danglingSequence'
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27 #end if
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28 --QCfolder ./QCfolder
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29
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30 --lines $lines
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31
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32 && mv ./QCfolder/* $qc.files_path/
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33 && mv $qc.files_path/hicQC.html $qc
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34 && mv $qc.files_path/*.log raw_qc
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35 ]]> </command>
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36 <inputs>
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37 <!-- can we use multiple="true" with min="2" and max="2" ? -->
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38 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
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39 <param name="samFile" type="data" format="sam,qname_input_sorted.bam" />
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40 </repeat>
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41 <expand macro="restrictionCutFile" />
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42 <expand macro="restrictionSequence" />
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43 <expand macro="danglingSequence" />
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44 <param argument="--lines" optional="true" type="integer" label="Lines to analyze for the QC report" help= "Number of lines to consider for the qc test run." value="1000000" />
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45 </inputs>
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46 <outputs>
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47 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
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48 <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" />
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49 </outputs>
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50 <tests>
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51 <test expect_num_outputs="2">
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52 <repeat name="samFiles">
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53 <param name="samFile" value="small_test_R1_unsorted.sam" />
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54 </repeat>
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55 <repeat name="samFiles">
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56 <param name="samFile" value="small_test_R2_unsorted.sam" />
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57 </repeat>
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58 <param name="restrictionCutFile" value="DpnII_10k.bed" />
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59 <param name="restrictionSequence" value="GATC" />
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60 <param name="danglingSequence" value="GATC" />
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61 <param name="lines" value="1000" />
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62 <output name="raw_qc" file="hicQuickQC/QC.log" compare="diff" lines_diff="2" />
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66
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67 Quick QC
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68 ========
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69
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70 Get a quick impression on the quality of your Hi-C data. hicQuickQC considers the first n lines of two bam/sam files to get a first estimate of the quality of the data. It is highly recommended to set the restriction enzyme and dangling end parameter to get a good quality report.
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71
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72 The default is to read the first 1,000,000 reads of the mapped bam files to get a quality estimate of the Hi-C data.
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73
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74 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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75
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76 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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77 ]]> </help>
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78 <expand macro="citations" />
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79 </tool>